Below is an error obtained from our galaxy install. We have custom
directories sets for the files directory and the jobs directory. Galaxy
appears to move the files but then attempts to look for them at the
original path. I have tried unsetting these options but the issue of it looking in the jobs_directory after the file has already been moved still persists.

It looks like you're using the outputs_to_working_directory option in galaxy.ini? It looks like what's happening here is that Galaxy detects that setting metadata on the job's output datasets has failed and it's trying to do it again on the Galaxy server (retry_metadata_internally, which defaults to True).

I believe you've encountered a bug in this scenario, but it'd be good to know why setting metadata failed when the job was run on the cluster. You should find in the job's directory files named like metadata_results_HistoryDatasetAssociation_<id>_<random_chars>, this should contain an error if setting metadata failed. It might also be displayed just a few lines up in the log you've pasted.